The mother of Erika Perez Escobedo looks at Brian Maguire's portrait of her daughter, one of the 1,400 women murdered in Ciudad Juárez in the last 20 years.

Bertha Alicia contemplates the portrait of her murdered daughter, Brenda Berenice, at first with little expression on her face. Then she nods approvingly, turns to the wall of her little home in Ciudad Juárez, Mexico, and takes down a picture of a chicken from Looney Tunes that is hanging there, and puts the portrait in its place. It is as though the dead Brenda had, in some form, returned home.

Brenda is one of some 1,400 factory girls working in Juárez who have been abducted, violated, mutilated and killed since the so-called feminocidio began in 1994. The scene, which arrives towards the end of Blood Rising, a new documentary about the slaughter by director Mark McLoughlin, is so poignant one has to turn away from the screen. Brian Maguire, the Irish artist who painted the portrait of Brenda for her mother, and who collaborated on the film with McLoughlin, clearly feels similarly. In the scene, he stands ill at ease as Bertha thanks him for the portrait and hugs him; the embrace is utterly sincere, almost desperate, from both sides.

"Brian was so relieved, he hugged her so hard he nearly strangled her," says McLoughlin. In an earlier scene, mother and painter had sat together on a sofa talking about Brenda's life and death, and they joined hands. Then they continued to sit, intimately but awkwardly, not knowing what to do, not wanting to let go.

I know that feeling, from reporting the feminocidio for this newspaper and later for a book – that of total but unbearable immersion in this appalling narrative. So does any writer, film-maker, painter who confronts this depth of depravity.

There have been several attempts – on screen and on the page – to convey the horror and the disbelief of the feminocidio and the humbling defiance of the dead girls' mothers. But McLoughlin's film is in a class of its own in showing and handling not only the barbarism of its subject matter, but its delicacy, and the sensitivities inherent in covering it at all. As Maguire learned while painting portraits of prisoners in the jails of Ireland, as he did for many years, the sitters stay, he goes home. Narrators of stories of this kind, if they care, have a fear of exploiting grief as they walk the high wire between narrative and voyeurism. For the first time in a report on the feminocidio by foreigners, manipulation is entirely absent from the telling.

This is in part due to the craftsmanship of its visual narration. And it's in part due to the extraordinary undertaking of the film's "presenter", Maguire, who tasked himself to paint (in a way that becomes all-consuming, almost obsessive) portraits of scores of these murdered girls. These portraits he then presented to the girls' mothers.

Blood Rising was premiered in Dublin last year at a packed screening presented by a mother called Elia Escobedo García whose 29-year-old daughter, Erika, was one of those abducted, tortured and murdered. The Dublin screening was followed by another in Galway at which Elia and the director broke down, leaving the "entire audience in tears", as McLoughlin recalls. Its UK premiere was at the Soho Curzon last month; soon it will tour Britain, presented by Elia and Bertha Alicia, mother of Brenda Berenice Castillo García.

Erika Perez Escobedo, 29, found murdered in Ciudad Juárez in 2002. Brian Maguire's portrait of her was later presnted to her family. Photograph: Brian Maguire

Stories about the feminocidio in Ciudad Juárez emerged slowly during the late 1990s, not least because media and observers across the border in America were unable to grasp serial violence of this nature and scale. By 2002, when I went to report the story, 340 young women had been murdered in ways that beggared belief. The figure of murdered women has now reached 1,400. Equally but differently shocking was the response of the local, state and national authorities: they were not merely indifferent, but blocked any attempt to track the killers. There were convincing signs that these authorities were sometimes behind the death threats to any mother or activist who tried to seek justice.

The girls were invariably captured while running errands in the centre of town, or on their way to or from work in the hundreds of maquiladoras: sweatshop assembly plants that constitute the economy of Juárez, manufacturing (for rock-bottom wages) the goods that America and Europe deem essential to keep their supermarket shelves and car-concession outlets stocked. The reactions to the killings of their employees by the multinational corporations that own the factories has ranged from callous indifference to offensive disregard.

One 16-year-old, sexually assaulted and murdered, was last seen in a police station. And after the murder of Erika Perez Escobedo a modest monument was built, later bulldozed into the dust. In McLoughlin's film, Erika's mother, Elia, lays flowers on the rubble left behind. The murdered girls are blamed for going out alone and their parents for allowing them. "The message," says Maguire, "is that here you can kill working-class women with impunity."

By the close of 2007, the slaughter of these women became subsumed within the wider carnage of Mexico's drug war, which has to date claimed some 100,000 lives, with an estimated 20,000 missing, and which for many years made Juárez the murder capital of the world.

There were connections between the feminocidio and the drug war. First, in what Mexican-American anthropologist and writer Cecilia Ballí calls the "style of killing", whereby the perverse ferocity of the narco war (its mutilations and decapitations) seems to have been "predicted" by that of the feminocidio. Second, and more directly, some of the murders of women seemed to have been committed by members of an embryonic branch of the Juárez narco-trafficking cartel called La Línea, the Line, whose executioners overlapped with local police forces.

Among the many themes with which Blood Rising grapples is that the feminocidio, far from being ended by the narco war, continued and continues within it. Appearing in the film, Julian Cardona, a former maquiladora worker-turned-photographer, stands at the rubbish dump where the first body was found in 1994. He says: "It begins here. It continues and it doesn't look like it's going to stop."

Brian Maguire was born in Dublin, to a family from Fermanagh in Northern Ireland, in 1951. In the early years of the Troubles, he joined the leftist Official Republican Movement, from which the militant Provisionals split in 1969, and which declared an early ceasefire in 1972.

Maguire started exhibiting during the 1980s, depicting what one of his exhibition catalogues called "various incarcerated groups on the island of Ireland, from mental hospitals to prisons". Critics refer to Maguire's style as "neoexpressionist", meaning, presumably, that his paintings stand in defiance of what another catalogue calls the "ragbag of postmodernism", favouring instead emotional gravitas and physical mass. Maguire, compelled towards the raw realities of prisons and mental institutions, describes himself as "entirely outside that new British school of art which has left reality, [which is] all kitsch and commodity". Maguire is substance, the real thing.

His portraits deploy bold strokes. His palettes superimpose cold greys and greens on to warm pink flesh to depict a blighted, often sepulchral human species. Suddenly, there'll be a head sculptured in charcoal and blue gouache, deep-toned and severe, but beautiful. One of his prison projects was a residency for the 1998 Bienal in São Paulo, Brazil; reflecting the haunting aftermath of a prison riot, Maguire painted bodies in boxes against vortices of grey masonry and vast but stifling space.

Maguire says he tries to work within his own rules of commercial engagement – "to be in situations," as he describes it to me, "where there is no charge for the paintings themselves. This is work for which I am paid a wage, and the painting itself has no value to me. It is free to the person whom I've painted. There've been occasions when the paintings ended up in auctions – but it's the prisoner selling the work, not me."

Around a decade after the São Paulo residency, his Juárez project began. Maguire was there, not for the customary weeks and months that reporters like me invest, but for four years. "When I heard about what was happening in Juárez," says Maguire, "I figured, of course – women come below men, poor come below rich, brown comes below white and Mexico comes below America. They don't fucking count, and that is why they die." He says he learned that "these people wanted their story told, in the event of their being no justice for them. The only thing they ask is that the memory of their daughters, and the actions done to them, not disappear with their deaths."

In the case of Brenda Berenice Castillo García, Maguire says: "I was in a state of cold fury. Here was a 16-year-old, the age at which women in Juárez begin to make families. But unlike women in the Netherlands or France, the law is not applied [in Brenda's case], she is denied maternity leave and laid off by her employer, Philips, because she's pregnant. There's no money for milk to give baby Kevin, so she goes in search of work at a jewellery store – and disappears."

Maguire made his Juárez portraits in pairs, one to exhibit, the other for the families to keep. They are more intimate and closely focused than his previous work, lighter of touch, but no less impactful. Two years into the project, he was joined in Mexico by director McLoughlin. Together they started filming Blood Rising.

"The killings of these women in Juárez were not tit-for-tat killings," says McLoughlin. "They are killings at a level of psychic perversion I simply couldn't understand. And that was the challenge. We had to take this on board emotionally. We built relationships with the mothers and families, but all the time this anger and fear was building up, frustration and bewilderment. And you take on the fear and grief of the people themselves, until sometimes you'd hit an emotional brick wall, out of exhaustion. Brian would call me up and say, 'I've been crying, have you?' And I'd answer, 'Yes, I have.'"

Guadelupe Verónica Castro Pando, 18, killed in 1996 in Lomas de Poleo, on the outskirts of Juárez. Photograph: Brian Maguire

In the film, we learn little details of the horrors: Erika Perez Escobedo was found in the street, strangled, her underwear disturbed; Guadalupe Verónica Castro Pando was abused and drugged for 21 days, and her left breast was cut off before she was buried alive. But the film is really about struggle and defiance, not the crimes themselves. "The mothers bring us on a journey back," says Maguire, "to where their daughters were murdered, where they were found, what the state did and did not do." Violence is not the subject of this film; the subject is the surviving mothers, families and friends and their struggle to live on.

"Most work," Maguire says in the film, "is a negotiation, most work is an exchange... [One in which] you have to give something back." During a Q&A with the audience after the London screening of Blood Rising, he added that the murdered girls' families "were in our hands, and we were in their hands too. They had to trust that we would not exploit them".

In conversation with me, Maguire expands on this. "You have to bring some value to the place and people, which gives you the right to work there. And that value can be negotiated. For a start, I can take their story outside Mexico, and tell it to Europe… I can campaign for them by showing my paintings in museums… I try to give something to their children." The artist not only paints the portraits, he also teaches the children of the murdered girls. One of the film's most heart-rending scenes shows one of these art classes and the joy these children experience when painting.

After years of conversation with the mother of one victim, Maguire says: "I have some idea as regard [the victim's] personality. And I also have a photographic image. I felt that if I had some relationship with their relatives, then, and only then, I could paint their portraits."

There is something talismanic about Maguire's recreations by portrait. In the film, we see him pacing around his studio in which he based himself across the border in El Paso, Texas, covering its walls with victims' photographs, writing their names in enraged grief, and setting to work.

Watching Blood Risingand talking to Maguire, a thought occurred to me, forcefully. Mexico is a country in which the image of the Virgin of Guadalupe is more important to most people than God himself. Popular faith in Mexico tends to be "folk Catholicism"; it is by no means entirely separated from Aztec and Mayan beliefs, nor the lore and deities that preceded the Hispanic Christianity that incorporated them. Popular faith in Mexico is sensitive to the occult, the veil between the living and the dead thin. The image, the icon, is everything.

Painting two portraits of each selected victim, Maguire often seems to create one of a girl's life and the other of her death; one portraying effervescence, the other murder. This is the case with Brenda. The first portrait, in monochrome, shows her features distorted only slightly but in such a way that vividly and disconcertingly seems to convey her doom. Another, in colour, exudes the life of the young woman. Brenda's mother, recounts Maguire, "saw the black-and-white picture, but she wanted something that recalled her living child. She had another photograph, from school days – and from that I painted the second in colour, which she put on the wall. However, I did notice a copy of the first on her dresser – I felt strangely gratified that she wanted that portrait too, but privately."

There are two ways to report or film crimes such as the Juárez feminocidio. One is to convey some distant horror, exotic in its way, in places or circumstances separated from our own by Manichaean morality; some evil in Mexico, against which our legitimate society, appalled, campaigns or crusades.

The other way is to insist – as writers such as Roberto Saviano in Italy or Anabel Hernández in Mexico do, and as Maguire does passionately in this film – that these atrocious narratives are integral to our own routines; that the blood stains our everyday lives; that "this is not another world", as Maguire told his audience during the Soho Q&A, "it is directly connected to our world, in fact it is our world. It's right under the bonnet of your car."

When we sit down to talk he says: "Juárez is not happenstance, it's part of an economic construct, our economic construct. These girls make those things like the electrical distributors in cars, they make all the junk – everything – we use all the time. Juárez is a city that does not care about its people, [who are] human fodder for the factories. They're now building a new factory to make iPads and things, 25 miles out in the desert from Juárez. That's 50 miles a day by bus for the workers to and from a place with no shops, nothing but the factory, to be paid less now than they were 10 years ago. It's our system. It's the telephone I talk on."

And in this statement lies the final, haunting theme in Blood Rising and in Maguire's art – which happens to be the story of my own life: the feeling of ineffectuality, the impotent pointlessness of this work; these films, these paintings, writing articles, books, whatever. On his last night at work on the portraits, Maguire recalls: "I was having dinner alone in the safety of El Paso. After four years, it was over. There were two emotions: one happy, that I'd had the experience, and that we'd made the film. But also: it's worthless, it's meaningless, it's nothing. We are totally ineffective.

"The mothers have been glad to see us, and I'll tell their story. But there is this sense of total helplessness. All I know for certain is that more poor factory girls will die in Ciudad Juárez, and that those iPads will be all shiny and new. So I went back to Juárez in despair and Julian Cardona, the photographer, rescued me. 'Look, Brian,' he said, 'let's just do our work as best we can, shall we?'"